User: bioinformatics

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Posts by bioinformatics

<prev • 16 results • page 2 of 2 • next >
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EdgeR two condition problem
... Hello !    I have used DESeq and EdgeR to get differentially expressed genes.    For DESeq it is possible to put a design with more conditions.  This is important because the data i used has    for example treated and untreated columns. But also differences in  cells types. And also the way ...
edger written 3.0 years ago by bioinformatics • 10 • updated 3.0 years ago by Aaron Lun • 25k
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Meta-analysis on rna-seq data without replicates
... Hello !    I have four data-sets. These data-sets are from different studies and or cell strains. Two of them do only have a control and a treated vector.   I was following the default approach for the meta-analysis for rna-seq :  https://cran.r-project.org/web/packages/metaRNASeq/vignettes/me ...
rnaseq meta-analysis metarnaseq written 3.1 years ago by bioinformatics • 10 • updated 3.1 years ago by Michael Love ♦ 26k
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Most efficient way to remove genes that are in a string of another fector
... Hey !    I have a deseq object ( not ran the deseq pipeline yet).  Because i want to compare rna-seq data from different sources, i want to remove the genes that are non-protein coding. This is due to wanting cleaner data ( some rna is rrna ).    So i downloaded the gene information for homo-s ...
deseq2 R written 3.2 years ago by bioinformatics • 10 • updated 3.2 years ago by Michael Love ♦ 26k
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Comment: A: rnaseq with DESeq am i doing it right ?
... ​Thanks for your response ! ...
written 3.2 years ago by bioinformatics • 10
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DESeq RNA-seq with different datasets
... Hello ! I have RNA-seq data from different cell strains/tissues. The datasets differ in the following way: dataset a : two columns: one treated and one untreated. dataset b : 3 treated 2 untreated. dataset c : 4 treated 4 untreated. I merged all datasets together so it has 15 columns. Currently i ...
deseq2 written 3.2 years ago by bioinformatics • 10 • updated 3.2 years ago by Michael Love ♦ 26k
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rnaseq with DESeq am i doing it right ?
... I am trying to find new markers for senescent cells. There are multiple datasets i made with fibroblast cells. The difference in the datasets is for example dataset 1 has to measurements. One with data from a young cell, and one from an senescent cell. Some datasets have 2 of young and 1 of senesce ...
rnaseq deseq2 written 3.2 years ago by bioinformatics • 10

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